Chlamydia trachomatis is the most common sexually transmitted bacterial pathogen in the U.S. with an annual incidence of 5 million cases. Studies have been in progress to define the clinical spectrum of chlamydial infection, to develop improved diagnostic assays and to examine the pathogenesis of chlamydial infections. In screening 10,000 patients attending STD clinics, we have demonstrated that molecular amplification assays, including polymerase chain reaction (PCR) and ligase chain reaction (LCR), have markedly improved the sensitivity of detection of C. trachomatis. In screening urine samples by PCR or LCR, the prevalence of chlamydia infection was 14% among women attending STD clinics, 8% in family planning clinics, and 11% in adolescent high school clinics. In a new assay in which we co-amplify by PCR for detection of N. gonorrhoeae and C. trachomatis in male and female urine, infection rates were as high as 33.9% and 24.4% for chlamydia and gonorrhea among STD patients in the Philippines, Jamaica, and Malaysia. In transmission studies of 460 sexual partnerships, 52% were concordantly PCR positive. In contrast to culture results, the transmission efficiency was equal bidirectionally at 68%. In preliminary studies it appears that local production of TGF-beta in a predominant Th1 response to chlamydial infection is highly associated with the development of both an inflammatory and follicular trachoma, eventually leading to corneal scarring and blindness. Following our development of PCR for C. pneumoniae, we have identified C. pneumoniae in 8% of 700 patients with respiratory disease, with rates as high as 35% among immunocompromised patients. In vitro studies have demonstrated replication of C. pneumoniae in human pulmonary macrophages, human pulmonary artery endothelial cells, aortic artery endothelial cells, and aortic artery smooth muscle cells. After screening approximately 50 individuals with severe coronary atherosclerosis, we have demonstrated by culture, PCR, electron microscopy, and in situ hybridization, the presence of C. trachomatis in coronary atheromas in six patients. Additional studies are planned to further address the role of C. pneumoniae in respiratory disease and atherosclerotic heart disease.